Preheat the oven to 350 degrees F. Prepare a 12 muffin tin with paper liners. Note: if you do not use paper liners, the baking time will be different.
Place the dry ingredients in one bowl and wet ingredients in another bowl. Combine the wet ingredients with the dry ingredients and use a teaspoon to portion the mixture into the cupcake liners, filling them about 3/4 of the way.
Transfer the cupcakes to the oven and bake for 31 minutes or until golden brown. Stick a knife in the center of the cupcakes to make sure they are done.
Remove from the oven; set aside for 20 minutes at room temperature and then ice with the frosting. Top with the coconut flakes and serve. Store leftover cupcakes in the refrigerator for up to 5 days in a sealed container.